Incidental Mutation 'R7661:Nanog'
ID 591564
Institutional Source Beutler Lab
Gene Symbol Nanog
Ensembl Gene ENSMUSG00000012396
Gene Name Nanog homeobox
Synonyms ENK, 2410002E02Rik, ecat4
MMRRC Submission 045736-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7661 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 122684448-122691592 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 122690431 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Tryptophan at position 279 (R279W)
Ref Sequence ENSEMBL: ENSMUSP00000012540 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000012540] [ENSMUST00000112580] [ENSMUST00000112581]
AlphaFold Q80Z64
PDB Structure CRYSTAL STRUCTURE OF THE NANOG HOMEODOMAIN [X-RAY DIFFRACTION]
Predicted Effect probably damaging
Transcript: ENSMUST00000012540
AA Change: R279W

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: R279W

DomainStartEndE-ValueType
low complexity region 13 25 N/A INTRINSIC
HOX 96 158 5.33e-22 SMART
low complexity region 206 230 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000112580
AA Change: R254W

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: R254W

DomainStartEndE-ValueType
HOX 71 133 5.33e-22 SMART
low complexity region 181 205 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000112581
AA Change: R254W

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: R254W

DomainStartEndE-ValueType
HOX 71 133 5.33e-22 SMART
low complexity region 181 205 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 96% (50/52)
MGI Phenotype FUNCTION: The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a disruption in this gene die between E3.5 and E5.5 with abnormal embryonic and extraembryonic tissue development. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3110018I06Rik A T 12: 107,455,215 (GRCm39) K100N unknown Het
Abi3bp T A 16: 56,453,263 (GRCm39) probably null Het
Akr1c20 T C 13: 4,558,218 (GRCm39) D210G probably benign Het
Arid5b C T 10: 67,934,417 (GRCm39) G495E probably benign Het
Ascc1 A C 10: 59,885,629 (GRCm39) N227H probably damaging Het
Atp5f1a G T 18: 77,861,802 (GRCm39) A18S possibly damaging Het
Bcl2l13 A G 6: 120,842,558 (GRCm39) T84A possibly damaging Het
Blmh T A 11: 76,877,341 (GRCm39) V419D probably damaging Het
Cacna1d G A 14: 29,769,177 (GRCm39) P1918S probably benign Het
Calr4 T C 4: 109,110,951 (GRCm39) V339A probably benign Het
Capza3 C A 6: 139,987,498 (GRCm39) D32E probably benign Het
Cilk1 G C 9: 78,074,902 (GRCm39) V586L probably benign Het
Cldn20 T A 17: 3,583,133 (GRCm39) M102K possibly damaging Het
Dennd1a T C 2: 37,734,841 (GRCm39) Q479R probably benign Het
Dpp10 A T 1: 123,312,681 (GRCm39) I432N probably damaging Het
Dst T A 1: 34,295,434 (GRCm39) probably null Het
Efcab3 T A 11: 104,617,503 (GRCm39) D741E probably benign Het
Fam135a C T 1: 24,111,843 (GRCm39) probably null Het
Fam47e C T 5: 92,735,384 (GRCm39) L206F probably damaging Het
Focad G A 4: 88,221,772 (GRCm39) R714H unknown Het
Hace1 T G 10: 45,481,649 (GRCm39) V124G probably damaging Het
Ifit1bl2 T A 19: 34,596,428 (GRCm39) Y396F probably damaging Het
Il22ra2 A G 10: 19,497,826 (GRCm39) I13M probably benign Het
Kif21a A G 15: 90,865,122 (GRCm39) F517L possibly damaging Het
Lrrc4 T C 6: 28,829,762 (GRCm39) T618A probably benign Het
Mdn1 A G 4: 32,691,229 (GRCm39) T952A probably benign Het
Mindy3 A T 2: 12,402,328 (GRCm39) I208K probably damaging Het
Mug1 C A 6: 121,838,179 (GRCm39) H470N possibly damaging Het
Mycbp2 A G 14: 103,450,059 (GRCm39) I1744T probably damaging Het
Ncoa2 T A 1: 13,244,761 (GRCm39) T646S probably damaging Het
Ndufa5 A G 6: 24,518,724 (GRCm39) *117R probably null Het
Nudt18 A T 14: 70,817,276 (GRCm39) E293D probably benign Het
Or1e22 A G 11: 73,377,426 (GRCm39) S75P probably damaging Het
Or51aa2 A T 7: 103,187,826 (GRCm39) V205E probably damaging Het
Paip1 C T 13: 119,587,306 (GRCm39) T390I possibly damaging Het
Pigg G A 5: 108,486,485 (GRCm39) V713I probably benign Het
Pih1d2 T C 9: 50,529,558 (GRCm39) probably null Het
Ppp2r3d A G 9: 124,442,696 (GRCm38) F17L Het
Ptprk T C 10: 28,342,036 (GRCm39) I481T probably benign Het
Pygo2 T C 3: 89,338,038 (GRCm39) probably null Het
Raet1d T C 10: 22,248,156 (GRCm39) S225P possibly damaging Het
Rnf24 T C 2: 131,164,135 (GRCm39) probably benign Het
Ror1 A G 4: 100,298,687 (GRCm39) S687G probably damaging Het
Rsph9 A G 17: 46,446,013 (GRCm39) S186P probably damaging Het
Sash1 C T 10: 8,605,155 (GRCm39) M1078I probably benign Het
Scd4 C A 19: 44,327,510 (GRCm39) D195E probably benign Het
Spopfm3 C T 3: 94,105,709 (GRCm39) T9I probably damaging Het
Syn3 A G 10: 85,904,940 (GRCm39) C348R probably damaging Het
Uspl1 T C 5: 149,151,827 (GRCm39) F1009S probably benign Het
Vmn1r2 T A 4: 3,172,149 (GRCm39) F23I probably benign Het
Vmn1r257 A G 7: 22,391,229 (GRCm39) S172P probably benign Het
Vmn2r-ps158 T A 7: 42,672,582 (GRCm39) N72K probably benign Het
Zfp747l1 A T 7: 126,984,135 (GRCm39) C322* probably null Het
Zfp839 C T 12: 110,835,226 (GRCm39) T827I probably benign Het
Other mutations in Nanog
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00475:Nanog APN 6 122,688,495 (GRCm39) critical splice acceptor site probably null
IGL03278:Nanog APN 6 122,688,704 (GRCm39) missense probably damaging 1.00
IGL03387:Nanog APN 6 122,688,731 (GRCm39) missense probably damaging 1.00
R0280:Nanog UTSW 6 122,690,357 (GRCm39) missense probably damaging 0.96
R1443:Nanog UTSW 6 122,688,734 (GRCm39) missense probably damaging 1.00
R2520:Nanog UTSW 6 122,690,418 (GRCm39) missense probably benign 0.08
R3037:Nanog UTSW 6 122,690,227 (GRCm39) missense possibly damaging 0.81
R4486:Nanog UTSW 6 122,689,676 (GRCm39) critical splice donor site probably null
R4770:Nanog UTSW 6 122,688,550 (GRCm39) missense possibly damaging 0.63
R4790:Nanog UTSW 6 122,684,874 (GRCm39) missense probably benign 0.00
R4825:Nanog UTSW 6 122,690,299 (GRCm39) missense probably benign 0.09
R4931:Nanog UTSW 6 122,684,865 (GRCm39) missense possibly damaging 0.95
R6010:Nanog UTSW 6 122,690,255 (GRCm39) missense probably benign 0.16
R6025:Nanog UTSW 6 122,690,350 (GRCm39) missense possibly damaging 0.94
R8236:Nanog UTSW 6 122,690,131 (GRCm39) missense probably benign
R8272:Nanog UTSW 6 122,688,736 (GRCm39) missense probably benign 0.00
R8520:Nanog UTSW 6 122,690,475 (GRCm39) missense possibly damaging 0.94
R9500:Nanog UTSW 6 122,690,219 (GRCm39) missense probably damaging 1.00
R9632:Nanog UTSW 6 122,684,799 (GRCm39) missense probably benign 0.00
R9710:Nanog UTSW 6 122,684,799 (GRCm39) missense probably benign 0.00
X0065:Nanog UTSW 6 122,684,752 (GRCm39) missense probably benign
Z1176:Nanog UTSW 6 122,690,190 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TGGACCAACCCAACTTGGA -3'
(R):5'- GTCTCCAAAGCCTAGAGTTAACA -3'

Sequencing Primer
(F):5'- CCCAACTTGGAGCAGCC -3'
(R):5'- TGCAGAGAAACCCTGTCTTG -3'
Posted On 2019-11-12